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Yorodumi- PDB-7wdu: 6-sulfo-beta-D-N-acetylglucosaminidase from Bifidobacterium bifid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wdu | |||||||||
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Title | 6-sulfo-beta-D-N-acetylglucosaminidase from Bifidobacterium bifidum in complex with PUGNAc-6S | |||||||||
Components | Beta-N-acetylhexosaminidaseHexosaminidase | |||||||||
Keywords | HYDROLASE / Glycoside hydrolase family 20 | |||||||||
Function / homology | Function and homology information glycosaminoglycan metabolic process / ganglioside catabolic process / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / beta-N-acetylglucosaminidase activity / lysosome / carbohydrate metabolic process / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Bifidobacterium bifidum JCM 1254 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.23 Å | |||||||||
Authors | Kashima, T. / Yamada, C. / Fushinobu, S. / Katoh, T. / Katayama, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Nat.Chem.Biol. / Year: 2023 Title: A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem. Authors: Katoh, T. / Yamada, C. / Wallace, M.D. / Yoshida, A. / Gotoh, A. / Arai, M. / Maeshibu, T. / Kashima, T. / Hagenbeek, A. / Ojima, M.N. / Takada, H. / Sakanaka, M. / Shimizu, H. / Nishiyama, ...Authors: Katoh, T. / Yamada, C. / Wallace, M.D. / Yoshida, A. / Gotoh, A. / Arai, M. / Maeshibu, T. / Kashima, T. / Hagenbeek, A. / Ojima, M.N. / Takada, H. / Sakanaka, M. / Shimizu, H. / Nishiyama, K. / Ashida, H. / Hirose, J. / Suarez-Diez, M. / Nishiyama, M. / Kimura, I. / Stubbs, K.A. / Fushinobu, S. / Katayama, T. #1: Journal: Biosci Biotechnol Biochem / Year: 2017 Title: Identification and characterization of a sulfoglycosidase from Bifidobacterium bifidum implicated in mucin glycan utilization. Authors: Katoh, T. / Maeshibu, T. / Kikkawa, K.I. / Gotoh, A. / Tomabechi, Y. / Nakamura, M. / Liao, W.H. / Yamaguchi, M. / Ashida, H. / Yamamoto, K. / Katayama, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wdu.cif.gz | 169.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wdu.ent.gz | 132.2 KB | Display | PDB format |
PDBx/mmJSON format | 7wdu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/7wdu ftp://data.pdbj.org/pub/pdb/validation_reports/wd/7wdu | HTTPS FTP |
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-Related structure data
Related structure data | 7wdtC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 89778.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium bifidum JCM 1254 (bacteria) Gene: bbhII / Plasmid: pET23b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): delta-lacZ-CodonPlus / References: UniProt: D4QAP5, beta-N-acetylhexosaminidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% (w/v) PEG3000, 0.1 M sodium citrate pH 5.5, 1 mM PUGNAc-6S |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2019 |
Radiation | Monochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→49.31 Å / Num. obs: 37545 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.11 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.079 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.23→2.3 Å / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3437 / CC1/2: 0.796 / Rpim(I) all: 0.353 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.23→48.36 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.4 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 154.65 Å2 / Biso mean: 36.494 Å2 / Biso min: 23.5 Å2
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Refinement step | Cycle: final / Resolution: 2.23→48.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.23→2.288 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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